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Many systems on our planet are known to shift abruptly and irreversibly from one state to another when they are forced across a tipping point, such as mass extinctions in ecological networks, cascading failures in infrastructure systems, and social convention changes in human and animal networks. Such a regime shift demonstrates a systems resilience that characterizes the ability of a system to adjust its activity to retain its basic functionality in the face of internal disturbances or external environmental changes. In the past 50 years, attention was almost exclusively given to low dimensional systems and calibration of their resilience functions and indicators of early warning signals without considerations for the interactions between the components. Only in recent years, taking advantages of the network theory and lavish real data sets, network scientists have directed their interest to the real-world complex networked multidimensional systems and their resilience function and early warning indicators. This report is devoted to a comprehensive review of resilience function and regime shift of complex systems in different domains, such as ecology, biology, social systems and infrastructure. We cover the related research about empirical observations, experimental studies, mathematical modeling, and theoretical analysis. We also discuss some ambiguous definitions, such as robustness, resilience, and stability.
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Exploiting recent developments in information theory, we propose, illustrate, and validate a principled information-theoretic algorithm for module discovery and resulting measure of network modularity. This measure is an order parameter (a dimensionless number between 0 and 1). Comparison is made to other approaches to module-discovery and to quantifying network modularity using Monte Carlo generated Erdos-like modular networks. Finally, the Network Information Bottleneck (NIB) algorithm is applied to a number of real world networks, including the social network of coauthors at the APS March Meeting 2004.
Networks are at the core of modeling many engineering contexts, mainly in the case of infrastructures and communication systems. The resilience of a network, which is the property of the system capable of absorbing external shocks, is then of paramount relevance in the applications. This paper deals with this topic by advancing a theoretical proposal for measuring the resilience of a network. The proposal is based on the study of the shocks propagation along the patterns of connections among nodes. The theoretical model is tested on the real-world instances of two important airport systems in the US air traffic network; Illinois (including the hub of Chicago) and New York states (with JFK airport).
This note discusses a theoretical issue regarding the application of the Modular Response Analysis method to quasi-steady state (rather than steady-state) data.
The simulation of complex stochastic network dynamics arising, for instance, from models of coupled biomolecular processes remains computationally challenging. Often, the necessity to scan a models dynamics over a large parameter space renders full-fledged stochastic simulations impractical, motivating approximation schemes. Here we propose an approximation scheme which improves upon the standard linear noise approximation while retaining similar computational complexity. The underlying idea is to minimize, at each time step, the Kullback-Leibler divergence between the true time evolved probability distribution and a Gaussian approximation (entropic matching). This condition leads to ordinary differential equations for the mean and the covariance matrix of the Gaussian. For cases of weak nonlinearity, the method is more accurate than the linear method when both are compared to stochastic simulations.
Many diseases display heterogeneity in clinical features and their progression, indicative of the existence of disease subtypes. Extracting patterns of disease variable progression for subtypes has tremendous application in medicine, for example, in early prognosis and personalized medical therapy. This work present a novel, data-driven, network-based Trajectory Clustering (TC) algorithm for identifying Parkinsons subtypes based on disease trajectory. Modeling patient-variable interactions as a bipartite network, TC first extracts communities of co-expressing disease variables at different stages of progression. Then, it identifies Parkinsons subtypes by clustering similar patient trajectories that are characterized by severity of disease variables through a multi-layer network. Determination of trajectory similarity accounts for direct overlaps between trajectories as well as second-order similarities, i.e., common overlap with a third set of trajectories. This work clusters trajectories across two types of layers: (a) temporal, and (b) ranges of independent outcome variable (representative of disease severity), both of which yield four distinct subtypes. The former subtypes exhibit differences in progression of disease domains (Cognitive, Mental Health etc.), whereas the latter subtypes exhibit different degrees of progression, i.e., some remain mild, whereas others show significant deterioration after 5 years. The TC approach is validated through statistical analyses and consistency of the identified subtypes with medical literature. This generalizable and robust method can easily be extended to other progressive multi-variate disease datasets, and can effectively assist in targeted subtype-specific treatment in the field of personalized medicine.
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